GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DUF4157 - Domain of unknown function (DUF4157)
Pfam: PF13699 (v27) Consensus Sequence
Download Alignment
(Note: includes all positions in family; we filtered this alignment to remove sites that had > 75% gaps before running GREMLIN. )
Clan: CL0126
Length: 79
Sequences: 611
Seq/Len: 7.73
HH_delta: 0.774 (20Jul13)
GREMLIN Results:
Residue pairs sorted by strength in covariance:

Legend: The darker and larger the blue dots, the higher strength in covariance. Below we provide the list of the top [1.5 x length] gremlin predictions, sequence seperation > 3. The i and j are positions as given in the consensus sequence. Show Scaled Distribution

ij Raw Score Scaled Score
39_R53_K0.553873.211
32_A41_F0.434822.521
3_P6_I0.419622.433
10_L69_L0.417132.418
7_R11_E0.391442.269
24_H46_D0.349762.028
9_R13_A0.332491.928
9_R62_R0.31641.834
65_L69_L0.306361.776
6_I9_R0.298741.732
20_D76_R0.298381.730
32_A48_Y0.288291.671
10_L18_L0.265951.542
33_A41_F0.259471.504
30_S50_A0.257821.495
58_S61_G0.257561.493
18_L69_L0.243341.411
4_E8_S0.220261.277
61_G65_L0.215471.249
11_E18_L0.212151.230
20_D45_N0.204521.186
6_I65_L0.204231.184
42_T72_V0.202951.177
33_A48_Y0.196761.141
8_S12_R0.196381.138
49_F61_G0.19621.137
5_S12_R0.193871.124
11_E47_I0.19171.111
45_N73_V0.186781.083
33_A70_A0.180851.048
2_L66_A0.178771.036
14_F47_I0.170290.987
14_F18_L0.168830.979
31_R34_A0.168830.979
23_V47_I0.168580.977
14_F73_V0.166190.963
42_T75_Q0.163760.949
49_F64_L0.163590.948
20_D77_R0.162570.942
10_L13_A0.158220.917
13_A66_A0.157740.914
25_T49_F0.155680.903
4_E45_N0.152520.884
11_E14_F0.150180.871
30_S59_P0.149340.866
12_R20_D0.147830.857
23_V41_F0.147690.856
59_P62_R0.146380.849
24_H40_A0.140010.812
4_E60_E0.139160.807
17_D20_D0.138770.805
9_R43_V0.137460.797
38_A75_Q0.137430.797
36_L63_A0.137380.796
41_F72_V0.136430.791
45_N76_R0.136090.789
2_L69_L0.135540.786
44_G75_Q0.133980.777
33_A43_V0.132550.768
24_H52_G0.131750.764
52_G59_P0.131650.763
23_V65_L0.128430.745
14_F70_A0.127370.738
7_R18_L0.127120.737
30_S61_G0.125890.730
10_L66_A0.125860.730
16_A39_R0.125490.728
40_A49_F0.12420.720
17_D22_R0.1240.719
73_V77_R0.123860.718
70_A73_V0.123540.716
9_R12_R0.122270.709
40_A52_G0.122130.708
13_A73_V0.120490.699
61_G64_L0.120410.698
16_A20_D0.120280.697
31_R51_P0.119440.692
40_A44_G0.119250.691
5_S9_R0.11910.690
15_G41_F0.117310.680
30_S63_A0.116470.675
6_I14_F0.11610.673
14_F74_Q0.115580.670
7_R19_S0.114840.666
44_G48_Y0.113620.659
50_A58_S0.113540.658
11_E65_L0.113130.656
32_A43_V0.112960.655
21_V69_L0.112160.650
9_R20_D0.112120.650
9_R47_I0.112030.649
37_G51_P0.111720.648
32_A35_A0.110930.643
10_L73_V0.110150.639
22_R46_D0.109480.635
43_V62_R0.109280.634
38_A47_I0.109180.633
39_R47_I0.109050.632
49_F62_R0.10790.626
42_T77_R0.106970.620
66_A69_L0.106950.620
23_V34_A0.106630.618
34_A43_V0.106590.618
38_A52_G0.10650.617
Legend: The value of the raw score is the function of the learning procedure, L2 normalization and APC (entropic) correction. These are to be used for relative ranking only.
HHsearch Results:
Top (length/2) GREMLIN results overlayed on top 10 PDB hits:

Legend: The grey circles underneath are pdb residue contacts (min distance < 5 Angstroms). The coloring of these circles is based on HHsearch results which uses the overall probability, per-site alignment prob and agreement of top hits weighted by HHsearch score (Note we only consider monomeric contacts, there might be homo-oligomeric contacts in the pdb that are not shown.)
PDB Cov Prob HH_delta
3cqbA0.886195.20.774
3c37A0.886194.70.781
4il3A0.936794.70.782
4aw6A0.936794.60.782
4jiuA0.898790.10.812
4jixA0.898789.60.814
3ebhA0.911483.30.83
2gtqA0.911482.70.831
3se6A0.911482.40.831
3nqxA0.898781.60.833
If you are interested in a protein containing this domain,
drop us a note and we'll try to predict the structure for you.

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